After the Infinite Tsukuyomi is activated, the user manipulates the roots of the Shinju, spreading them around the entire world to encase those caught within the genjutsu. By ensnaring all living beings and connecting them to the tree, similar to cocoons, this will keep their now-slumbering bodies alive for all of eternity. At the same time, this assimilates every victim to the Shinju, regathering the chakra into one location, in order to sprout a new fruit.

The chakra can also be collectively used by the user of this technique, as proven when Madara Uchiha's body began to rapidly absorb the chakra of everyone connected to the tree during his transformation into Kaguya Ōtsutsuki. According to Black Zetsu, over an unspecified amount of time, those ensnared by this technique will be converted into White Zetsu.

According to Minato Namikaze, simply cutting the victims loose neither wake them up, nor free them from the tree, as another branch will simply form and imprison them once again.[2]

Once the Infinite Tsukuyomi is cancelled, the branches, along with any preexisting White Zetsu, wither away and the entrapped people would be freed, assuming they have not already been converted to White Zetsu.[3]